[1] Capo FC was founded in 2006 with the mission of developing the youth soccer in the southern part of Orange County, California.

[3][4] In June 2020, the team was accepted in the United Premier Soccer League with plans to begin play in Division 1 for the Fall 2020 season.

The team was promoted to the Premier Division for Fall 2021 where it finished the regular season undefeated in the SoCal North Conference.

On November 30, 2021, the club announced it would join NISA Nation as members of its brand new Southwest Region.

The club's crest features the bell tower of Mission Basilica San Juan Capistrano flanked by two cliff swallows, similar to those on the city's flag.